scholarly journals Backbone and nearly complete side-chain chemical shift assignments of the human death-associated protein 1 (DAP1)

2020 ◽  
Author(s):  
Christoph Wiedemann ◽  
Johanna Voigt ◽  
Jan Jirschitzka ◽  
Sabine Häfner ◽  
Oliver Ohlenschläger ◽  
...  
Keyword(s):  
Chemical Shift ◽  
Chemical Shifts ◽  
Intrinsically Disordered Protein ◽  
Potential Interaction ◽  
Chemical Shift Assignments ◽  
Cell Growth And Migration ◽  
Structural Investigations ◽  
Intrinsically Disordered ◽  
Spectral Dispersion ◽  
And Migration

AbstractDeath-associated protein 1 (DAP1) is a proline-rich cytoplasmatic protein highly conserved in most eukaryotes. It has been reported to be involved in controlling cell growth and migration, autophagy and apoptosis. The presence of human DAP1 is associated to a favourable prognosis in different types of cancer. Here we describe the almost complete $${{^{1}}\text {H}}$$ 1 H , $${{^{13}}\text {C}}$$ 13 C , and $${{^{15}}\text {N}}$$ 15 N chemical shift assignments of the human DAP1. The limited spectral dispersion, mainly in the $${{^{1}}\text {H}{^{\text{N}}}}$$ 1 H N region, and the lack of defined secondary structure elements, predicted based on chemical shifts, identifies human DAP1 as an intrinsically disordered protein (IDP). This work lays the foundation for further structural investigations, dynamic studies, mapping of potential interaction partners or drug screening and development.

scholarly journals Backbone and nearly complete side-chain chemical shift assignments reveal the human uncharacterized protein CXorf51A as intrinsically disordered

2021 ◽  
Vol 15 (2) ◽  
pp. 441-448
Author(s):  
Christoph Wiedemann ◽  
Kingsley Benjamin Obika ◽  
Sandra Liebscher ◽  
Jan Jirschitzka ◽  
Oliver Ohlenschlãger ◽  
...  
Keyword(s):  
Chemical Shift ◽  
Intrinsically Disordered Protein ◽  
Genome Project ◽  
Side Chain ◽  
Resonance Spectroscopy ◽  
Chemical Shift Assignments ◽  
Uncharacterized Protein ◽  
Protein Coding ◽  
Intrinsically Disordered ◽  
Side Chain Chemical Shift

AbstractEven though the human genome project showed that our DNA contains a mere 20,000 to 25,000 protein coding genes, an unexpectedly large number of these proteins remain functionally uncharacterized. A structural characterization of these “unknown” proteins may help to identify possible cellular tasks. We therefore used a combination of bioinformatics and nuclear magnetic resonance spectroscopy to structurally de-orphanize one of these gene products, the 108 amino acid human uncharacterized protein CXorf51A. Both our bioinformatics analysis as well as the $$^1$$ 1 H, $$^{13}$$ 13 C, $$^{15}$$ 15 N backbone and near-complete side-chain chemical shift assignments indicate that it is an intrinsically disordered protein.

scholarly journals Bayesian-Maximum-Entropy reweighting of IDP ensembles based on NMR chemical shifts

2019 ◽  
Author(s):  
Ramon Crehuet ◽  
Pedro J. Buigues ◽  
Xavier Salvatella ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Chemical Shift ◽  
Maximum Entropy ◽  
Chemical Shifts ◽  
Intrinsically Disordered Protein ◽  
Intrinsically Disordered ◽  
Computational Data ◽  
Chemical Shift Data ◽  
Secondary Chemical Shifts ◽  
Validation Set ◽  
Secondary Chemical

AbstractBayesian and Maximum Entropy approaches allow for a statistically sound and systematic fitting of experimental and computational data. Unfortunately, assessing the relative confidence in these two types of data remains difficult as several steps add unknown error. Here we propose the use of a validation-set method to determine the balance, and thus the amount of fitting. We apply the method to synthetic NMR chemical shift data of an intrinsically disordered protein. We show that the method gives consistent results even when other methods to assess the amount of fitting cannot be applied. Finally, we also describe how the errors in the chemical shift predictor can lead to an incorrect fitting and how using secondary chemical shifts could alleviate this problem.

scholarly journals Bayesian-Maximum-Entropy Reweighting of IDP Ensembles Based on NMR Chemical Shifts

Entropy ◽  
2019 ◽  
Vol 21 (9) ◽  
pp. 898 ◽  
Author(s):  
Ramon Crehuet ◽  
Pedro J. Buigues ◽  
Xavier Salvatella ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Chemical Shift ◽  
Maximum Entropy ◽  
Chemical Shifts ◽  
Intrinsically Disordered Protein ◽  
Intrinsically Disordered ◽  
Computational Data ◽  
Chemical Shift Data ◽  
Secondary Chemical Shifts ◽  
Validation Set ◽  
Secondary Chemical

Bayesian and Maximum Entropy approaches allow for a statistically sound and systematic fitting of experimental and computational data. Unfortunately, assessing the relative confidence in these two types of data remains difficult as several steps add unknown error. Here we propose the use of a validation-set method to determine the balance, and thus the amount of fitting. We apply the method to synthetic NMR chemical shift data of an intrinsically disordered protein. We show that the method gives consistent results even when other methods to assess the amount of fitting cannot be applied. Finally, we also describe how the errors in the chemical shift predictor can lead to an incorrect fitting and how using secondary chemical shifts could alleviate this problem.

scholarly journals Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation

2019 ◽  
Vol 116 (41) ◽  
pp. 20446-20452 ◽  
Author(s):  
Utsab R. Shrestha ◽  
Puneet Juneja ◽  
Qiu Zhang ◽  
Viswanathan Gurumoorthy ◽  
Jose M. Borreguero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Intrinsically Disordered Proteins ◽  
Chemical Shifts ◽  
Intrinsically Disordered Protein ◽  
Physical Models ◽  
Dynamics Simulation ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Eukaryotic Proteomes ◽  
Heterogeneous Ensemble

Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes, play a major role in cell signaling, and are associated with human diseases. To understand IDP function it is critical to determine their configurational ensemble, i.e., the collection of 3-dimensional structures they adopt, and this remains an immense challenge in structural biology. Attempts to determine this ensemble computationally have been hitherto hampered by the necessity of reweighting molecular dynamics (MD) results or biasing simulation in order to match ensemble-averaged experimental observables, operations that reduce the precision of the generated model because different structural ensembles may yield the same experimental observable. Here, by employing enhanced sampling MD we reproduce the experimental small-angle neutron and X-ray scattering profiles and the NMR chemical shifts of the disordered N terminal (SH4UD) of c-Src kinase without reweighting or constraining the simulations. The unbiased simulation results reveal a weakly funneled and rugged free energy landscape of SH4UD, which gives rise to a heterogeneous ensemble of structures that cannot be described by simple polymer theory. SH4UD adopts transient helices, which are found away from known phosphorylation sites and could play a key role in the stabilization of structural regions necessary for phosphorylation. Our findings indicate that adequately sampled molecular simulations can be performed to provide accurate physical models of flexible biosystems, thus rationalizing their biological function.

scholarly journals Random coil chemical shifts for serine, threonine and tyrosine phosphorylation over a broad pH range

2019 ◽  
Vol 73 (12) ◽  
pp. 713-725 ◽  
Author(s):  
Ruth Hendus-Altenburger ◽  
Catarina B. Fernandes ◽  
Katrine Bugge ◽  
Micha B. A. Kunze ◽  
Wouter Boomsma ◽  
...  
Keyword(s):  
Chemical Shift ◽  
Secondary Structure ◽  
Intrinsically Disordered Proteins ◽  
Chemical Shifts ◽  
Random Coil ◽  
Disordered Proteins ◽  
Phosphoryl Group ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Secondary Chemical

Abstract Phosphorylation is one of the main regulators of cellular signaling typically occurring in flexible parts of folded proteins and in intrinsically disordered regions. It can have distinct effects on the chemical environment as well as on the structural properties near the modification site. Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins (IDPs) and the reliability of the analysis depends on an appropriate choice of random coil model. Random coil chemical shifts and sequence correction factors were previously determined for an Ac-QQXQQ-NH2-peptide series with X being any of the 20 common amino acids. However, a matching dataset on the phosphorylated states has so far only been incompletely determined or determined only at a single pH value. Here we extend the database by the addition of the random coil chemical shifts of the phosphorylated states of serine, threonine and tyrosine measured over a range of pH values covering the pKas of the phosphates and at several temperatures (www.bio.ku.dk/sbinlab/randomcoil). The combined results allow for accurate random coil chemical shift determination of phosphorylated regions at any pH and temperature, minimizing systematic biases of the secondary chemical shifts. Comparison of chemical shifts using random coil sets with and without inclusion of the phosphoryl group, revealed under/over estimations of helicity of up to 33%. The expanded set of random coil values will improve the reliability in detection and quantification of transient secondary structure in phosphorylation-modified IDPs.

scholarly journals De Novo Generation of Bound Structures for an Intrinsically Disordered Protein using Only Alpha Carbon Chemical Shifts

2013 ◽  
Vol 104 (2) ◽  
pp. 191a
Author(s):  
F. Marty Ytreberg ◽  
Stepan Kashtanov ◽  
Wade Borcherds ◽  
Hongwei Wu ◽  
Gary W. Daughdrill
Keyword(s):  
De Novo ◽  
Chemical Shifts ◽  
Intrinsically Disordered Protein ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Alpha Carbon

scholarly journals 1H, 13C, and 15N backbone chemical shift assignments of the C-terminal dimerization domain of SARS-CoV-2 nucleocapsid protein

2020 ◽  
Author(s):  
Sophie M. Korn ◽  
Roderick Lambertz ◽  
Boris Fürtig ◽  
Martin Hengesbach ◽  
Frank Löhr ◽  
...  
Keyword(s):  
Chemical Shift ◽  
Nucleocapsid Protein ◽  
Rna Binding ◽  
Drug Binding ◽  
Chemical Shift Assignments ◽  
Binding Studies ◽  
Dimerization Domain ◽  
N Protein ◽  
Intrinsically Disordered ◽  
Backbone Chemical Shift

AbstractThe current outbreak of the highly infectious COVID-19 respiratory disease is caused by the novel coronavirus SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2). To fight the pandemic, the search for promising viral drug targets has become a cross-border common goal of the international biomedical research community. Within the international Covid19-NMR consortium, scientists support drug development against SARS-CoV-2 by providing publicly available NMR data on viral proteins and RNAs. The coronavirus nucleocapsid protein (N protein) is an RNA-binding protein involved in viral transcription and replication. Its primary function is the packaging of the viral RNA genome. The highly conserved architecture of the coronavirus N protein consists of an N-terminal RNA-binding domain (NTD), followed by an intrinsically disordered Serine/Arginine (SR)-rich linker and a C-terminal dimerization domain (CTD). Besides its involvement in oligomerization, the CTD of the N protein (N-CTD) is also able to bind to nucleic acids by itself, independent of the NTD. Here, we report the near-complete NMR backbone chemical shift assignments of the SARS-CoV-2 N-CTD to provide the basis for downstream applications, in particular site-resolved drug binding studies.

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